fixes while testing 1.33.0

[mothur.git] / systemcommand.h

diff --git a/systemcommand.h b/systemcommand.h
index 55b772b71ddaa62767746d7543f61ae09a5b5e39..27adf7c5993289bc0edeeb9f56b8de5939b2bfb0 100644 (file)
--- a/systemcommand.h
+++ b/systemcommand.h
@@ -18,20 +18,25 @@ class SystemCommand : public Command {
        public:
        
                SystemCommand(string);  
-               SystemCommand() { abort = true; calledHelp = true; }
+               SystemCommand() { setParameters(); abort = true; calledHelp = true; }
                ~SystemCommand(){}
-               vector<string> getRequiredParameters();
-               vector<string> getValidParameters();
-               vector<string> getRequiredFiles();
-               map<string, vector<string> > getOutputFiles() { return outputTypes; }
-               int execute();
-               void help();    
-               
+       
+               vector<string> setParameters();
+               string getCommandName()                 { return "system";              }
+               string getCommandCategory()             { return "General";             }
+        string getHelpString();        
+        string getOutputPattern(string){ return ""; }  
+               string getCitation() { return "http://www.mothur.org/wiki/System"; }
+               string getDescription()         { return "execute system commands from within mothur"; }
+
+               int execute(); 
+               void help() { m->mothurOut(getHelpString()); }  
+       
        private:
                string command;
                bool abort;
                vector<string> outputNames;
-               map<string, vector<string> > outputTypes;
+               
                
 };